In 1943, General Huebner relieved the popular commander of the 1st Infantry Division, General Terry Allen, in a move engineered by General Omar N. Bradley. While the 1st ID, aka The Big Red One had enjoyed considerable combat success under Allen's leadership, Bradley was highly critical of both Allen and Roosevelt's wartime leadership style, which favored fighting ability over drill and discipline: "While the Allies were parading decorously through Tunis," Bradley wrote, "Allen's brawling 1st Infantry Division was celebrating the Tunisian victory in a manner all its own. In towns from Tunisia all the way to Arzew, the division had left a trail of looted wine shops and outraged mayors. But it was in Oran...that the division really ran amuck. The trouble began when SOS (Services of Supply) troops, long stationed in Oran, closed their clubs and installations to our combat troops from the front. Irritated by this exclusion, the 1st Division swarmed into town to 'liberate' it a second time."[2][3] Despite this, Bradley admitted that "none excelled the unpredictable Terry Allen in the leadership of troops."[4]

Upon assuming command, General Huebner immediately ordered a series of close-order drills, parades, and weapons instruction for the 1st ID, including its veterans, who had just finished a bloody series of engagements with German forces in Sicily. This did not endear him to the enlisted men of the division, who made no attempt to hide their preference for General Allen.[5] As one of the men of the Big Red One said in disgust, "Hell's bells! We've been killing Germans for months and now they are teaching us to shoot a rifle? It doesn't make any sense."[6]

Supported by Bradley and Eisenhower, Huebner persisted, and the morale of the division gradually recovered. As the commander of the "Big Red One" in World War II, Huebner led the 1st in the assault on Omaha Beach, followed by a successful infantry attack at Saint-Lô. The 1st would later repel a German counteroffensive at Mortain, and pursue the German Army across France, culminating in the Battles of Aachen and the Huertgen Forest.

After World War II, Huebner was the last Military Governor (acting) of the American Zone in Germany from May 15, 1949, to September 1, 1949. He retired in 1950. On September 1, 1951, he became director of New York State's Civil Defense Commission, a post he held until January 1961. A strong advocate of the building of fallout shelters, General Huebner believed the US population would eventually be forced to live full-time in underground shelters and "would see the sunshine only by taking a calculated risk".

Huebner married Florence Barrett in 1921. Following her death in 1966, Huebner married Anna Imelda Mathews in 1968. She died in 1974. All three are buried together in Arlington National Cemetery.